John Quackenbush

John Quackenbush

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John Quackenbush

Publications by authors named "John Quackenbush"

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Gaussian and Mixed Graphical Models as (multi-)omics data analysis tools.

Biochim Biophys Acta Gene Regul Mech 2019 Oct 19:194418. Epub 2019 Oct 19.

Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17475 Greifswald, Germany. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S18749399193022
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http://dx.doi.org/10.1016/j.bbagrm.2019.194418DOI Listing
October 2019

lionessR: single sample network inference in R.

BMC Cancer 2019 Oct 25;19(1):1003. Epub 2019 Oct 25.

Channing Division of Network Medicine, Brigham and Women's Hospital, 181 Longwood Avenue, Boston, 02215, USA.

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http://dx.doi.org/10.1186/s12885-019-6235-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6815019PMC
October 2019

Clinical and Molecular Analysis of Pathologic Fracture-associated Osteosarcoma: MicroRNA profile Is Different and Correlates with Prognosis.

Clin Orthop Relat Res 2019 Sep;477(9):2114-2126

S. A. Lozano Calderón, J. Kim, K. Raskin, J. Schwab, D. Spentzos, Department of Orthopaedic Surgery, Musculoskeletal Oncology Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA Y.-L. Chen, K. Bernstein, T. Delaney, Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA I. Chebib, G. P. Nielsen, V. Deshpande, Department of Pathology, Bone and Soft Tissue Service, Massachusetts General Hospital, Harvard Medical School, Boston, MA R. Rubio, Y. E. Wang, J. Quackenbush, Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute, Boston, MA R. Rubio, Y. E. Wang, J. Quackenbush, Department of Biostatistics, Harvard School of Public Health, Boston, MA C. Garbutt, C. E. Lietz, G. Cote, Department of Medical Oncology, Massachusetts General Hospital, Boston, MA; Department of Medical Oncology, Massachusetts General Hospital, Boston, MA.

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http://dx.doi.org/10.1097/CORR.0000000000000867DOI Listing
September 2019

Identification of differentially expressed gene sets using the Generalized Berk-Jones statistica.

Bioinformatics 2019 May 7. Epub 2019 May 7.

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1093/bioinformatics/btz277DOI Listing
May 2019

Estimating Sample-Specific Regulatory Networks.

iScience 2019 Apr 28;14:226-240. Epub 2019 Mar 28.

Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.isci.2019.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6463816PMC
April 2019

The kinetic requirements of extreme qPCR.

Biomol Detect Quantif 2019 Mar 13;17:100081. Epub 2019 Mar 13.

Department of Pathology, University of Utah Health Sciences Center, Salt Lake City, UT, 84108, United States.

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http://dx.doi.org/10.1016/j.bdq.2019.100081DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6591793PMC
March 2019

Data Analysis Strategies in Medical Imaging.

Clin Cancer Res 2018 08 26;24(15):3492-3499. Epub 2018 Mar 26.

Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-18-0385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082690PMC
August 2018

Artificial intelligence in radiology.

Nat Rev Cancer 2018 08;18(8):500-510

Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

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http://www.nature.com/articles/s41568-018-0016-5
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http://dx.doi.org/10.1038/s41568-018-0016-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6268174PMC
August 2018

Histopathological Image QTL Discovery of Immune Infiltration Variants.

iScience 2018 Jul 6;5:80-89. Epub 2018 Jul 6.

Center for Cancer Computational Biology and Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, MA 02215, USA; Department of Biostatistics, Harvard T.H. Chan School of Public Health, 667 Huntington Avenue, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.isci.2018.07.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6123851PMC
July 2018

Cancer subtype identification using somatic mutation data.

Br J Cancer 2018 05 16;118(11):1492-1501. Epub 2018 May 16.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://www.nature.com/articles/s41416-018-0109-7
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http://dx.doi.org/10.1038/s41416-018-0109-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5988673PMC
May 2018

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma.

J Allergy Clin Immunol 2018 04 20;141(4):1250-1258. Epub 2017 Jul 20.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass. Electronic address:

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http://dx.doi.org/10.1016/j.jaci.2017.05.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5775928PMC
April 2018

Smooth quantile normalization.

Biostatistics 2018 04;19(2):185-198

Department of Computer Science, University of Maryland, College Park, USA and Center for Bioinformatics and Computational Biology, Institute of Advanced Computer Studies, University of Maryland, 8314 Paint Branch Dr., College Park, MD 20742, College Park, USA.

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http://dx.doi.org/10.1093/biostatistics/kxx028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5862355PMC
April 2018

Detecting phenotype-driven transitions in regulatory network structure.

NPJ Syst Biol Appl 2018 19;4:16. Epub 2018 Apr 19.

2Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA USA.

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http://dx.doi.org/10.1038/s41540-018-0052-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5908977PMC
April 2018

Estimating drivers of cell state transitions using gene regulatory network models.

BMC Syst Biol 2017 Dec 13;11(1):139. Epub 2017 Dec 13.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, 02115, MA, USA.

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http://dx.doi.org/10.1186/s12918-017-0517-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5729420PMC
December 2017

Cancer Informatics: New Tools for a Data-Driven Age in Cancer Research.

Cancer Res 2017 11;77(21):e1-e2

Dana-Farber Cancer Institute and Harvard TH Chan School of Public Health, Boston, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-2212DOI Listing
November 2017

WebMeV: A Cloud Platform for Analyzing and Visualizing Cancer Genomic Data.

Cancer Res 2017 11;77(21):e11-e14

Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0802DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5679251PMC
November 2017

Tissue-aware RNA-Seq processing and normalization for heterogeneous and sparse data.

BMC Bioinformatics 2017 Oct 3;18(1):437. Epub 2017 Oct 3.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.

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http://dx.doi.org/10.1186/s12859-017-1847-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627434PMC
October 2017

Understanding Tissue-Specific Gene Regulation.

Cell Rep 2017 Oct;21(4):1077-1088

Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2017.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828531PMC
October 2017

Exploring regulation in tissues with eQTL networks.

Proc Natl Acad Sci U S A 2017 09 29;114(37):E7841-E7850. Epub 2017 Aug 29.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1707375114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5604022PMC
September 2017

Regulatory network changes between cell lines and their tissues of origin.

BMC Genomics 2017 Sep 12;18(1):723. Epub 2017 Sep 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12864-017-4111-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596945PMC
September 2017

Expression Quantitative Trait loci (QTL) in tumor adjacent normal breast tissue and breast tumor tissue.

PLoS One 2017 2;12(2):e0170181. Epub 2017 Feb 2.

Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170181PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5289428PMC
August 2017

Estimating gene regulatory networks with pandaR.

Bioinformatics 2017 Jul;33(14):2232-2234

Department of Computational Biology and Biostatistics, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Boston, MA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btx139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5870629PMC
July 2017

Somatic Mutations Drive Distinct Imaging Phenotypes in Lung Cancer.

Cancer Res 2017 07 31;77(14):3922-3930. Epub 2017 May 31.

Department of Radiation Oncology Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.

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http://dx.doi.org/10.1158/0008-5472.CAN-17-0122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5528160PMC
July 2017

PyPanda: a Python package for gene regulatory network reconstruction.

Bioinformatics 2016 11 10;32(21):3363-3365. Epub 2016 Jul 10.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02215, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btw422DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5079480PMC
November 2016

Safikhani et al. reply.

Nature 2016 11;540(7631):E6-E8

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.

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http://dx.doi.org/10.1038/nature20172DOI Listing
November 2016

Safikhani et al. reply.

Nature 2016 11;540(7631):E11-E12

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.email:

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http://dx.doi.org/10.1038/nature20581DOI Listing
November 2016

Safikhani et al. reply.

Nature 2016 11;540(7631):E2-E4

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 2M9, Canada.

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http://dx.doi.org/10.1038/nature19839DOI Listing
November 2016

Diet-induced weight loss leads to a switch in gene regulatory network control in the rectal mucosa.

Genomics 2016 10 11;108(3-4):126-133. Epub 2016 Aug 11.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2016.08.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121035PMC
October 2016

Bipartite Community Structure of eQTLs.

PLoS Comput Biol 2016 09 12;12(9):e1005033. Epub 2016 Sep 12.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5019382PMC
September 2016

Epigenetic remodeling regulates transcriptional changes between ovarian cancer and benign precursors.

JCI Insight 2016 Aug;1(13)

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.; Harvard Medical School, Boston, Massachusetts, USA.; Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.

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http://dx.doi.org/10.1172/jci.insight.87988DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5017158PMC
August 2016

Assessment of pharmacogenomic agreement.

F1000Res 2016 9;5:825. Epub 2016 May 9.

Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada; Department of Computer Science, University of Toronto, Toronto, Ontario, M5S 2E4, Canada.

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http://dx.doi.org/10.12688/f1000research.8705.1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926729PMC
July 2016

Exploratory Study to Identify Radiomics Classifiers for Lung Cancer Histology.

Front Oncol 2016 30;6:71. Epub 2016 Mar 30.

Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.3389/fonc.2016.00071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4811956PMC
April 2016

Nac1 Coordinates a Sub-network of Pluripotency Factors to Regulate Embryonic Stem Cell Differentiation.

Cell Rep 2016 Feb 28;14(5):1181-1194. Epub 2016 Jan 28.

Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2015.12.101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749452PMC
February 2016

Integrating transcriptional and protein interaction networks to prioritize condition-specific master regulators.

BMC Syst Biol 2015 Nov 14;9:80. Epub 2015 Nov 14.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12918-015-0228-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4650867PMC
November 2015

Using shRNA experiments to validate gene regulatory networks.

Genom Data 2015 Jun 1;4:123-6. Epub 2015 Apr 1.

Bioinformatics and Computational Genomics Laboratory, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada ; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.

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http://dx.doi.org/10.1016/j.gdata.2015.03.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4535466PMC
June 2015

A network model for angiogenesis in ovarian cancer.

BMC Bioinformatics 2015 Apr 11;16:115. Epub 2015 Apr 11.

Dana-Farber Cancer Institute, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12859-015-0551-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408593PMC
April 2015

Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring.

Genome Med 2015 14;7(1):12. Epub 2015 Feb 14.

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA ; Division of Pulmonary and Critical Care Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA USA.

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http://dx.doi.org/10.1186/s13073-015-0137-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355149PMC
March 2015

Assessment of microRNA differential expression and detection in multiplexed small RNA sequencing data.

RNA 2015 Feb 17;21(2):164-71. Epub 2014 Dec 17.

Bioinformatics Graduate Program, Boston University, Boston, Massachusetts 02215, USA Section of Computational Biomedicine, Boston University Medical Center, Boston, Massachusetts 02118, USA Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, Massachusetts 02118, USA

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http://dx.doi.org/10.1261/rna.046060.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338344PMC
February 2015

Inference and validation of predictive gene networks from biomedical literature and gene expression data.

Genomics 2014 May-Jun;103(5-6):329-36. Epub 2014 Mar 29.

Computational Biology and Functional Genomics Laboratory, Dana-Farber Cancer Institute, Harvard School of Public Health, Boston, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119824PMC
January 2015

Sexually-dimorphic targeting of functionally-related genes in COPD.

BMC Syst Biol 2014 Nov 28;8:118. Epub 2014 Nov 28.

Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1186/s12918-014-0118-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4269917PMC
November 2014

Gene expression signature of normal cell-of-origin predicts ovarian tumor outcomes.

PLoS One 2013 26;8(11):e80314. Epub 2013 Nov 26.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America ; Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Brigham and Women's Hospital, Boston, Massachusetts, United States of America ; Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0080314PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3841174PMC
October 2014

Enhancing reproducibility in cancer drug screening: how do we move forward?

Cancer Res 2014 Aug 11;74(15):4016-23. Epub 2014 Jul 11.

Princess Margaret Cancer Centre, University Health Network; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada;

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http://dx.doi.org/10.1158/0008-5472.CAN-14-0725DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4119520PMC
August 2014

Gene expression variability as a unifying element of the pluripotency network.

Stem Cell Reports 2014 Aug 25;3(2):365-77. Epub 2014 Jul 25.

Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, Brisbane QSLD 4072, Australia; Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2014.06.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4175554PMC
August 2014

Comparative genome-wide transcriptional analysis of human left and right internal mammary arteries.

Genomics 2014 Jul 20;104(1):36-44. Epub 2014 May 20.

The Valley Columbia Heart Center, 223 North Van Dien Avenue Ridgewood, NJ 07450, USA; Columbia University College of Physicians and Surgeons, Department of Surgery, New York, NY 10032, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ygeno.2014.04.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4152843PMC
July 2014

Learning to share.

Authors:
John Quackenbush

Sci Am 2014 Jul;311(1):S22

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446053PMC
July 2014

Relevance of different prior knowledge sources for inferring gene interaction networks.

Front Genet 2014 24;5:177. Epub 2014 Jun 24.

Bioinformatics and Computational Genomics, Princess Margaret Cancer Centre, University Health Network Toronto, ON, Canada ; Medical Biophysics Department, University of Toronto Toronto, ON, Canada.

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http://dx.doi.org/10.3389/fgene.2014.00177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4067568PMC
July 2014

Perspective: Learning to share.

Authors:
John Quackenbush

Nature 2014 May;509(7502):S68

Center for Cancer Computational Biology at the Dana-Farber Cancer Institute in Boston, Massachusetts.

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http://dx.doi.org/10.1038/509S68aDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4205237PMC
May 2014

Differentiating progressive from nonprogressive T1 bladder cancer by gene expression profiling: applying RNA-sequencing analysis on archived specimens.

Urol Oncol 2014 Apr 18;32(3):327-36. Epub 2013 Sep 18.

Department of Urology, Massachusetts General Hospital and Harvard Medical School, Boston, MA. Electronic address:

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http://dx.doi.org/10.1016/j.urolonc.2013.06.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446054PMC
April 2014

A genome-wide aberrant RNA splicing in patients with acute myeloid leukemia identifies novel potential disease markers and therapeutic targets.

Clin Cancer Res 2014 Mar 27;20(5):1135-45. Epub 2013 Nov 27.

Authors' Affiliations: Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Bioinformatics and Computational Genomics Laboratory, Institut de Recherches Cliniques de Montréal, Montreal, Quebec, Canada; Department of Computing Science, University of Alberta, Edmonton, Alberta, Canada; Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; Dana-Farber Cancer Institute, Center for Cancer Systems Biology and Department of Genetics, Harvard Medical School, Boston University School of Medicine and Biomedical Engineering Department, Boston University, Boston, Massachusetts; Unité de Génomique du Myélome, Laboratoire UGM, University Hospital, CHU Rangueil, Toulouse, France; Hematology Laboratory, University Hospital; and INSERM U892, Nantes, France; Molecular Diagnostics Laboratory, Dana Farber Cancer Institute, Boston, Massachusetts; Biotique Systems Inc., www.biotiquesystems.com; Adult Leukemia Program, Dana Farber Cancer Institute, Boston, Massachusetts; Brigham and Women's Hospital, Boston, Massachusetts; Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts.

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http://dx.doi.org/10.1158/1078-0432.CCR-13-0956DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458245PMC
March 2014

Passing messages between biological networks to refine predicted interactions.

PLoS One 2013 31;8(5):e64832. Epub 2013 May 31.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0064832PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3669401PMC
January 2014

CXCR4 pathway associated with family history of melanoma.

Cancer Causes Control 2014 Jan 25;25(1):125-32. Epub 2013 Oct 25.

Department of Dermatology, Brigham and Women's Hospital, Harvard Medical School, 45 Francis St, 221L, Boston, MA, 02115, USA.

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http://dx.doi.org/10.1007/s10552-013-0315-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4100594PMC
January 2014

Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis.

PLoS One 2013 11;8(3):e57799. Epub 2013 Mar 11.

Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0057799PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3594231PMC
December 2013

Inconsistency in large pharmacogenomic studies.

Nature 2013 Dec 27;504(7480):389-93. Epub 2013 Nov 27.

1] Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [2] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA [3].

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http://dx.doi.org/10.1038/nature12831DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4237165PMC
December 2013

Accelerating genomic data publishing and sharing.

Genom Data 2013 Dec 28;1. Epub 2013 May 28.

Elsevier Publishing, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.gdata.2013.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608866PMC
December 2013

Epstein-Barr virus nuclear antigen leader protein localizes to promoters and enhancers with cell transcription factors and EBNA2.

Proc Natl Acad Sci U S A 2013 Nov 28;110(46):18537-42. Epub 2013 Oct 28.

Department of Medicine, Brigham and Women's Hospital, and Department of Microbiology and Immunobiology, Harvard University, Boston, MA 02115.

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http://dx.doi.org/10.1073/pnas.1317608110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3832032PMC
November 2013

Comparison and validation of genomic predictors for anticancer drug sensitivity.

J Am Med Inform Assoc 2013 Jul-Aug;20(4):597-602. Epub 2013 Jan 26.

Bioinformatics and Computational Genomics Laboratory, Institut de recherches cliniques de Montréal, University of Montreal, Montreal, Quebec, Canada.

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http://jamia.oxfordjournals.org/content/jaminfo/20/4/597.ful
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http://jamia.oxfordjournals.org/lookup/doi/10.1136/amiajnl-2
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http://dx.doi.org/10.1136/amiajnl-2012-001442DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3721163PMC
September 2013

Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance.

Genomics 2013 Jul 3;102(1):8-14. Epub 2013 Apr 3.

Division of Hematology/Oncology, Sarcoma Program, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, 330 Brookline Avenue, Boston, MA 02215, USA.

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http://dx.doi.org/10.1016/j.ygeno.2013.03.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116671PMC
July 2013

A tiered hidden Markov model characterizes multi-scale chromatin states.

Genomics 2013 Jul 6;102(1):1-7. Epub 2013 Apr 6.

Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA.

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http://dx.doi.org/10.1016/j.ygeno.2013.03.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3676702PMC
July 2013

Significance analysis of prognostic signatures.

PLoS Comput Biol 2013 24;9(1):e1002875. Epub 2013 Jan 24.

Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, Massachusetts, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3554539PMC
June 2013

Mutational analysis clopidogrel resistance and platelet function in patients scheduled for coronary artery bypass grafting.

Genomics 2013 Jun 24;101(6):313-7. Epub 2013 Feb 24.

Department of Biostatistics and Computational Biology and Center for Cancer Computational Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S08887543130003
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http://dx.doi.org/10.1016/j.ygeno.2013.01.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149181PMC
June 2013

Sequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma.

Clin Cancer Res 2013 May 14;19(9):2493-502. Epub 2013 Mar 14.

The Thoracic Surgery Oncology Laboratory, and International Mesothelioma Program, Division of Thoracic Surgery, Brigham and Women's Hospital, and Harvard Medical School, Boston, Massachusetts 02115, USA.

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http://dx.doi.org/10.1158/1078-0432.CCR-12-2117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3644001PMC
May 2013

RamiGO: an R/Bioconductor package providing an AmiGO visualize interface.

Bioinformatics 2013 Mar 6;29(5):666-8. Epub 2013 Jan 6.

School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland.

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http://dx.doi.org/10.1093/bioinformatics/bts708DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582261PMC
March 2013